rs726788

Variant names:

• chr19-14632433-A-G
• rs726788
• NM_032571.5:c.1643+488T>C

Your query was ambiguous. Multiple possible variants found:

• chr19-14632433-A-G
• chr19-14632433-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032571.5(ADGRE3):​c.1643+488T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 152,014 control chromosomes in the GnomAD database, including 19,127 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.50 (19127 hom., cov: 31)
• Consequence: ADGRE3 NM_032571.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170
• Publications: 10 publications found

Genes affected

ADGRE3 (HGNC:23647): (adhesion G protein-coupled receptor E3) This gene encodes a member of the class B seven-span transmembrane (TM7) receptor family expressed predominantly by cells of the immune system. Family members are characterized by an extended extracellular region with a variable number of N-terminal epidermal growth factor (EGF)-like domains coupled to a TM7 domain via a mucin-like spacer domain. This gene is closely linked to the gene encoding egf-like molecule containing mucin-like hormone receptor 2 on chromosome 19. This protein may play a role in myeloid-myeloid interactions during immune and inflammatory responses. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2014]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADGRE3	NM_032571.5	c.1643+488T>C		intron_variant	Intron 13 of 15	ENST00000253673.6	NP_115960.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADGRE3	ENST00000253673.6	c.1643+488T>C		intron_variant	Intron 13 of 15	1	NM_032571.5	ENSP00000253673.4

Frequencies

GnomAD3 genomes AF: 0.497 AC: 75482 AN: 151896 Hom.: 19117 Cov.: 31

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.506

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.497 AC: 75526 AN: 152014 Hom.: 19127 Cov.: 31 AF XY: 0.491 AC XY: 36484 AN XY: 74278

African (AFR) AF: 0.498 AC: 20668 AN: 41472

American (AMR) AF: 0.504 AC: 7682 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1630 AN: 3466

East Asian (EAS) AF: 0.209 AC: 1083 AN: 5178

South Asian (SAS) AF: 0.315 AC: 1517 AN: 4822

European-Finnish (FIN) AF: 0.497 AC: 5244 AN: 10560

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.530 AC: 36007 AN: 67954

Other (OTH) AF: 0.501 AC: 1057 AN: 2110

Alfa AF: 0.515 Hom.: 65335

Bravo AF: 0.502

Asia WGS AF: 0.296 AC: 1033 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.0
DANN	Benign	0.57
PhyloP100		-0.17
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs726788; hg19: chr19-14743245;